3 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	f0799f780b	rugnux: drop edge-of-sweep truncated fulls + honest R-meas over accepted obs ... From a fresh decomposition of the low-resolution-shell R-meas gap vs XDS on the reference lysozyme rotation crystal (7.6% vs 2.9%), two rot3d scale/merge changes: - New --min-captured-fraction (default 0.5 for rotation, off otherwise): drop a combined full whose rocking curve was captured below this fraction. These edge-of-sweep, partiality-extrapolated fulls (sweep start/end) are biased and inflate the low-res R-meas. Dropping them lowers low-shell R-meas 7.6->5.5% and *improves* external accuracy (CC vs the F-model and vs an independent dataset, and the ANODE anomalous S-peak 0.93->0.94x XDS) - unlike --min-partiality, which lowers R-meas cosmetically while degrading accuracy. Threaded through ScalingSettings and both the GPU and CPU combine. - R-meas reporting fix: the R_meas re-walk counted observations the merge had rejected as outliers (XDS excludes its misfits before its R-factor). The accumulate pass now flags each rejected full and the R_meas pass skips it, in both the GPU and CPU paths. Merged intensities / ISa / CC1/2 unchanged (verified byte-identical external accuracy); low-shell R-meas 7.6->6.5%. No-op when --reject-outliers 0. Combined default rotation low-shell R-meas 7.6->5.1%, ISa 17.2->17.5, external accuracy equal-or-better than baseline and XDS. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-10 20:13:06 +02:00
leonarski_fandClaude Opus 4.8	4f3153d6c7	rugnux: automatic CC1/2-logistic high-resolution cutoff ... Merge/report/write to the CC1/2 fall-off instead of the detector edge. After the final merge, fit a logistic to a fine-binned CC1/2 profile and cut one shell past cc_target (default 0.30) - generous, DIALS-style. Only the written MTZ/CIF and the reported shell table are trimmed; scaling, the 3D combine and the error model still run over the full range, and the per-image _process.h5 keeps full data for re-scaling. The de-novo P1 merge that feeds the space-group search is never cut (gated on the final merge). - ScalingSettings: resolution_cutoff {Off,CCHalfLogistic}, resolution_cc_target, report_shell_count (report shell count is now configurable). - New ResolutionCutoff.{h,cpp}: ComputeCCHalfLogisticCutoff (fine-bin CC1/2 + grid/refine logistic fit + one-shell extension + degeneracy/low-res guards). - Wired into RotationScaleMerge (rotation) and MergeOnTheFly/Rugnux (stills), plus the rugnux --scale path. - CLI: --resolution-cutoff cc-logistic|off, --resolution-cc-target, --resolution-shells. --scaling-high-resolution stays the manual override (wins and disables the auto-cut). Validated on the 24-crystal battery: no crashes (incl. Benas/cytC_10/Thau_9); --resolution-cutoff off is bit-identical to baseline; cutoffs reproduce the design table within ~0.05 A (lysoC 1.30, Ins_I 1.43, cytC_2 1.68, EcwtCQ244-E3 1.54); good-to-edge datasets (lyso_ref, EP_cs_02-10) correctly keep the full range. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-09 17:34:49 +02:00
leonarski_f	d6389e12da	v1.0.0-rc.156 (#66) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * jfjoch_process: Major rotation (rot3d) data processing overhaul - robust profile-fit integration, Cauchy-loss scaling with optional absorption surface, de-novo indexing and space-group/centering determination fixes, and merging statistics + ISa in the mmCIF output. * jfjoch_process: Add EXPERIMENTAL ice-ring detection (--detect-ice-rings) that excludes ice reflections from scaling. * Compression: Add BSHUF_ZSTD_RLE_HUFF, make compression size-aware (drop frames that don't fit rather than aborting), and add the jfjoch_recompress tool. * jfjoch_viewer: Report "Multiple lattices detected" and grey out "Analyze dataset" on a live connection. * jfjoch_broker: Write smargon chi/phi goniometer positions to NXmx; read sensor thickness/material from HDF5 metadata. * CI: Build Windows (CUDA and non-CUDA) installers.Reviewed-on: #66 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-03 19:18:56 +02:00